Locus 7228

Sequence ID dm3.chr3L
Location 13,176,392 – 13,176,570
Length 178
Max. P 0.745822
window9951 window9952

overview

Window 1

Location 13,176,392 – 13,176,471
Length 79
Sequences 12
Columns 82
Reading direction forward
Mean pairwise identity 79.50
Shannon entropy 0.42981
G+C content 0.41339
Mean single sequence MFE -15.98
Consensus MFE -8.27
Energy contribution -8.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.644950
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13176392 79 + 24543557
--UUGGGCGGGGAAAAAAAGGACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAAUACUCAGACAA-CACUAACCUCAA
--......((((........((((...((((((......))))))...))))(((...)))........-......)))).. ( -17.20, z-score =  -1.60, R)
>droSim1.chr3L 12571827 78 + 22553184
--UUGGGCGGGGAAAAAA-GGACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAAUACUCAAACAA-CACUAACCUCAA
--......((((......-.((((...((((((......))))))...))))(((...)))........-......)))).. ( -17.20, z-score =  -1.87, R)
>droSec1.super_0 5352151 78 + 21120651
--UUGGGCGGGGAAAAAA-GGACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAAUACUCAAACAA-CACUAACCUCAA
--......((((......-.((((...((((((......))))))...))))(((...)))........-......)))).. ( -17.20, z-score =  -1.87, R)
>droYak2.chr3L 13263008 77 + 24197627
--UUGGGCGAGGAAAAAG--GACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAAUACUCAGACAA-CACUAACCUCAA
--......((((......--((((...((((((......))))))...))))(((...)))........-......)))).. ( -18.10, z-score =  -2.02, R)
>droEre2.scaffold_4784 13184892 76 + 25762168
---UUGGCGAGGAAAAAG--GACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAAUACUCAGACAA-CACUAACCUCAA
---.....((((......--((((...((((((......))))))...))))(((...)))........-......)))).. ( -18.10, z-score =  -2.24, R)
>droAna3.scaffold_13337 10991025 68 - 23293914
-------------AAAAAAGGACAAACUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACUCAGGCAA-CACUAACCUCAA
-------------.......((((...((((((......))))))...))))............(....-)........... ( -13.70, z-score =  -1.20, R)
>dp4.chrXR_group6 5437614 80 + 13314419
--UGGCGCAGAAAAAAAAAGGACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACUCAGACAAACACUAACCUCAA
--.((...............((((...((((((......))))))...)))).....((......)).........)).... ( -12.60, z-score =  -0.14, R)
>droPer1.super_2858 1399 72 - 5027
----------UGGAAAAAAGGACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACUCAGACAAACACUAACCUCAA
----------.((.......((((...((((((......))))))...)))).....((......)).........)).... ( -13.30, z-score =  -0.99, R)
>droWil1.scaffold_180698 6693436 60 + 11422946
UCUUGAGUGGUAAAAAGG---ACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACCC-------------------
........((((...(.(---(((...((((((......))))))...)))).)....)))).------------------- ( -16.40, z-score =  -3.30, R)
>droVir3.scaffold_13049 12563149 71 + 25233164
--UUGAGUGGC-AAAAGG---ACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACCCAA-----CACUAACCCAAU
--...((((..-.....(---(((...((((((......))))))...))))(((...)))....-----))))........ ( -15.10, z-score =  -1.36, R)
>droMoj3.scaffold_6680 9886357 72 - 24764193
--UUGAGUGGC-GAAAGG---ACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACCCAAA----CACUAACCCAAA
--...((((.(-....)(---(((...((((((......))))))...))))..............----))))........ ( -17.80, z-score =  -2.18, R)
>droGri2.scaffold_15110 1411713 70 - 24565398
--UUGAGUGG--AAAAGG---ACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACCCAA-----CACUAGCCCAAA
--...((((.--.....(---(((...((((((......))))))...))))(((...)))....-----))))........ ( -15.10, z-score =  -1.46, R)
>consensus
__UUGGGCGGGGAAAAAA__GACAAAAUGUCACAAAAGCGUGACGAUGUGUCGUAAAGUACUCAGACAA_CACUAACCUCAA
.....................(((...((((((......))))))...)))............................... ( -8.27 =  -8.27 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,176,471 – 13,176,570
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 93.29
Shannon entropy 0.12102
G+C content 0.41350
Mean single sequence MFE -25.76
Consensus MFE -21.78
Energy contribution -23.18
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.745822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13176471 99 + 24543557
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUUCAAAGACCUCGAAACUUGGCUUUUUGUACUUUUCACUGGUCCUUUAGCUUAUGCUUGGAUACUCU
...(((((((.(((.(((((.....)))))..)))..)))))))((((....((.....))...))))....((((...(((....))).))))..... ( -24.90, z-score =  -2.42, R)
>droSim1.chr3L 12571905 98 + 22553184
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUUCAGAGACCUCGAAACUUGGCUUUU-GUACUUUUCACUGGUCCUUUAGCAUUUGCUUGGAUACCCU
...(((((((((((.(((((.....)))))..))).))))))))((((....((....-))...))))....((((...(((....))).))))..... ( -28.80, z-score =  -2.68, R)
>droSec1.super_0 5352229 98 + 21120651
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUUCAGAGACCUCGAAACUUGGCUUUU-GUACUUUUCACUGUUCCUCUAGCUUCUGCUUGGAUACCCU
...(((((((((((.(((((.....)))))..))).))))))))((((....((....-))...)))).....(((...(((....))).)))...... ( -27.30, z-score =  -2.51, R)
>droYak2.chr3L 13263085 98 + 24197627
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUCCAAAGACCUCGAACCUUGGCUUUU-GUACUUUUCACUGGUCCUGAAGCUUUUGCUUGGAUACCCU
..((((((((.(((.(((((.....))))).)))...))))))))..((..((((..(-(.......))..))))...((((....))))))....... ( -24.00, z-score =  -1.07, R)
>droEre2.scaffold_4784 13184968 98 + 25762168
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUUCAGAGAGCUCGAACCUUGGCUAUU-GUACUUUUCACUGGUCCUAAAGCUGUUGCUUGGAUACCCU
..((((.(((((((.(((((.....)))))..))).)))).))))..((..(((((.(-(.......)).)))))...((((....))))))....... ( -23.80, z-score =  -0.54, R)
>consensus
AAUGGGGUCUCGAAUGAUAUGGAAAAUGUCUUUUCAGAGACCUCGAAACUUGGCUUUU_GUACUUUUCACUGGUCCUUUAGCUUUUGCUUGGAUACCCU
...(((((((((((.(((((.....)))))..))).))))))))((((....((.....))...))))....((((...(((....))).))))..... (-21.78 = -23.18 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:56 2011